I am using limma for the detection of differentially expressed genes between two conditions. I have always been selecting the up- and down- regulated genes based on the logFC column of the topTable. However, today this column totally disappeared from the topTable output. Here is an example:
ID coef1 coef2 coef3 AveExpr F P.Value adj.P.Val 13910 NTSR1 -4.490258 -3.2078144 -3.7724694 9.746352 2577.270 3.960188e-30 6.338903e-26 8233 IL1B -2.650783 -5.7227167 -3.9875837 10.498109 2486.918 6.057530e-30 6.338903e-26 3360 COL13A1 -4.064761 -4.4417430 -3.2679355 9.823130 2345.764 1.214728e-29 8.474348e-26 10643 LOC643031 6.430895 -0.7497487 0.6393873 12.625948 1884.199 1.648177e-28 8.623672e-25 16631 S100A9 -4.186606 -3.5585657 -2.9390909 12.327986 1647.862 8.113864e-28 3.396301e-24 8232 IL1A -2.294970 -3.6533448 -4.0192784 9.810856 1493.671 2.608230e-27 9.097940e-24
I tried using the
resort.by arguments of topTable, trying to 'push' it display the logFC. But still, logFC was not there.
Has anyone encountered this before? I cannot get what has happened!
Thank you very much!
It would be helpful if you posted (A) the output of sessionInfo() and (B) the exact topTable command you used.
Yes, sure. Here is the output of
And here is the command that I used:
Thanks a lot for any feedback!
...Actually, when I use toptable, I don't have this problem. I can see the logFC column. But I don't prefer using it because:
a) It is deprecated and
b) I cannot make a calculation for all the coefficients of my contrast matrix simultaneously (as I can for topTable - default option for coef). I need to specify every time which coefficient I want to calculate and to combine each toptable's findings manually at the end...
Then post whatever command you are using, I just asked for topTable because that's what you originally wrote was being used.
I want to use topTable...Yes, please, answer to me regarding topTable. I would like to know why I cannot see the logFC column there. I just mentioned that when I use toptable I can see it...in case this is somehow informative about the source of the problem.
topTable and toptable produce different output, this is expected. See
help(topTable)for more information. Note that with more than one coefficient that
topTableF, which produces the coefficients rather than lfc between any particular coefficients (well, obviously these are the fold changes versus the intercept...).
Thank you, this is understandable. My worry is though why until some time ago, using exactly the same topTable command, I could see a logFC column and now I cannot. Any clues on that? I suspect I may have overwritten the original topTable function. If this is the case, I don't know how to fix it..If this is not the case, what else could it be?
Thank you very much!
Presumably you were using smaller models. topTable itself hasn't changed to my knowledge.
I was applying the topTable function on the same exact data, I was using exactly the same command. Maybe I accidentally did something wrong and overwritten it...I don't know how to convert it back so I see me switching to the use of toptable instead. Anyway, thank you for your time and help!